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SHOCK-INDUCED PORATION, CHOLESTEROL FLIP-FLOP
AND SMALL INTERFERING RNA TRANSFECTION IN A
PHOSPHOLIPID MEMBRANE: MULTIMILLION ATOM,
MICROSECOND MOLECULAR DYNAMICS SIMULATIONS
By
Amit Choubey
_____________________________________________________________________
A Dissertation Presented to the
FACULTY OF THE USC GRADUATE SCHOOL
UNIVERSITY OF SOUTHERN CALIFORNIA
In Partial Fulfillment of the
Requirements for the Degree
DOCTOR OF PHILOSOPHY
(PHYSICS)
May 2014
Copyright 2014 Amit Choubey

Biological cell membranes provide mechanical stability to cells and understanding their structure, dynamics and mechanics are important biophysics problems. Experiments coupled with computational methods such as molecular dynamics (MD) have provided insight into the physics of membranes. We use long‐time and large‐scale MD simulations to study the structure, dynamics and mechanical behavior of membranes. ❧ We investigate shock‐induced collapse of nanobubbles in water using MD simulations based on a reactive force field. We observe a focused jet at the onset of bubble shrinkage and a secondary shock wave upon bubble collapse. The jet length scales linearly with the nanobubble radius, as observed in experiments on micron‐to‐millimeter size bubbles. Shock induces dramatic structural changes, including an ice‐VII‐like structural motif at a particle velocity of 1 km/s. The incipient ice VII formation and the calculated Hugoniot curve are in good agreement with experimental results. We also investigate molecular mechanisms of poration in lipid bilayers due to shock‐induced collapse of nanobubbles. Our multimillion‐atom MD simulations reveal that the jet impact generates shear flow of water on bilayer leaflets and pressure gradients across them. This transiently enhances the bilayer permeability by creating nanopores through which water molecules translocate rapidly across the bilayer. Effects of nanobubble size and temperature on the porosity of lipid bilayers are examined. ❧ The second research project focuses on cholesterol (CHOL) dynamics in phospholipid bilayers. Several experimental and computational studies have been performed on lipid bilayers consisting of dipalmitoylphosphatidylcholine (DPPC) and CHOL molecules. CHOL interleaflet transport (flip-flop) plays an important role in interleaflet coupling and determining CHOL flip‐flop rate has been elusive. Various studies report that the rate ranges between milliseconds to seconds. We calculate CHOL flip‐flop rates by performing a 15 μs all‐atom MD simulation of a DPPC–CHOL bilayer. We find that the CHOL flip‐flop rates are on the sub microsecond timescale. These results are verified by performing various independent parallel replica (PR) simulations. Our PR simulations provide significant boost in sampling of the flip‐flop events. We observe that the CHOL flip‐flop can induce membrane order, regulate membrane‐bending energy, and facilitate membrane relaxation. The rapid flip‐flop rates reported here have important implications for the role of CHOL in mechanical properties of cell membranes, formation of domains, and maintaining CHOL concentration asymmetry in plasma membrane. Our PR approach can reach submillisecond time scales and bridge the gap between MD simulations and Nuclear Magnetic Resonance (NMR) experiments on CHOL flip‐flop dynamics in membranes. ❧ The last project deals with transfection barriers encountered by a bare small interfering RNA (siRNA) in a phospholipid bilayer. SiRNA molecules play a pivotal role in therapeutic applications. A key limitation to the widespread implementation of siRNA‐based therapeutics is the difficulty of delivering siRNA‐based drugs to cells. We have examined structural and mechanical barriers to siRNA passage across a phospholipid bilayer using all‐atom MD simulations. We find that the electrostatic interaction between the anionic siRNA and head groups of phospholipid molecules induces a phase transformation from the liquid crystalline to ripple phase. Steered MD simulations reveal that the siRNA transfection through the ripple phase requires a force of ~ 1.5 nN.

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SHOCK-INDUCED PORATION, CHOLESTEROL FLIP-FLOP
AND SMALL INTERFERING RNA TRANSFECTION IN A
PHOSPHOLIPID MEMBRANE: MULTIMILLION ATOM,
MICROSECOND MOLECULAR DYNAMICS SIMULATIONS
By
Amit Choubey
_____________________________________________________________________
A Dissertation Presented to the
FACULTY OF THE USC GRADUATE SCHOOL
UNIVERSITY OF SOUTHERN CALIFORNIA
In Partial Fulfillment of the
Requirements for the Degree
DOCTOR OF PHILOSOPHY
(PHYSICS)
May 2014
Copyright 2014 Amit Choubey